Jeffrey J. Gray, Ph.D. - Related publications

2002- Chemical & Biomolecular Engineering Johns Hopkins University, Baltimore, MD 
Protein docking, structure prediction and design, macromolecular assemblies
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50 most relevant papers in past 60 days:
Year Citation  Score
2019 Rubio AM, Rey A. Design of a structure-based model for protein folding from flexible conformations. Physical Chemistry Chemical Physics : Pccp. PMID 30848270 DOI: 10.1039/c9cp00168a   
2019 Kabir KL, Hassan L, Rajabi Z, Akhter N, Shehu A. Graph-Based Community Detection for Decoy Selection in Template-Free Protein Structure Prediction. Molecules (Basel, Switzerland). 24. PMID 30823390 DOI: 10.3390/molecules24050854   
2019 Peng Y, Alexov E, Basu S. Structural Perspective on Revealing and Altering Molecular Functions of Genetic Variants Linked with Diseases. International Journal of Molecular Sciences. 20. PMID 30696058 DOI: 10.3390/ijms20030548   
2019 Gao M, Zhou H, Skolnick J. DESTINI: A deep-learning approach to contact-driven protein structure prediction. Scientific Reports. 9: 3514. PMID 30837676 DOI: 10.1038/s41598-019-40314-1   
2019 Frezza E, Lavery R. Internal Coordinate Normal Mode Analysis: A Strategy to Predict Protein Conformational Transitions. The Journal of Physical Chemistry. B. PMID 30665293 DOI: 10.1021/acs.jpcb.8b11913   
2019 Ghosh P, Bhattacharyya T, Mathew OK, Sowdhamini R. PASS2 version 6: a database of structure-based sequence alignments of protein domain superfamilies in accordance with SCOPe. Database : the Journal of Biological Databases and Curation. 2019. PMID 30820573 DOI: 10.1093/database/baz028   
2019 Klausen MS, Jespersen MC, Nielsen H, Jensen KK, Jurtz VI, Sønderby CK, Sommer MOA, Winther O, Nielsen M, Petersen B, Marcatili P. NetSurfP-2.0: Improved prediction of protein structural features by integrated deep learning. Proteins. PMID 30785653 DOI: 10.1002/prot.25674   
2019 Han X, Li L, Lu Y. Selecting Near-Native Protein Structures from Predicted Decoy Sets Using Ordered Graphlet Degree Similarity. Genes. 10. PMID 30754721 DOI: 10.3390/genes10020132   
2019 Benini S, Haouz A, Proux F, Alzari P, Wilson K. The crystal structure of Rv2991 from Mycobacterium tuberculosis: an F binding protein with unknown function. Journal of Structural Biology. PMID 30890426 DOI: 10.1016/j.jsb.2019.03.006   
2019 Cui Y, Dong Q, Hong D, Wang X. Predicting protein-ligand binding residues with deep convolutional neural networks. Bmc Bioinformatics. 20: 93. PMID 30808287 DOI: 10.1186/s12859-019-2672-1   
2019 Keedy DA. Journey to the center of the protein: allostery from multitemperature multiconformer X-ray crystallography. Acta Crystallographica. Section D, Structural Biology. 75: 123-137. PMID 30821702 DOI: 10.1107/S2059798318017941   
2019 Taechalertpaisarn J, Lyu RL, Arancillo M, Lin CM, Perez LM, Ioerger TR, Burgess K. Correlations between secondary structure- and protein-protein interface-mimicry: the interface mimicry hypothesis. Organic & Biomolecular Chemistry. PMID 30847453 DOI: 10.1039/c9ob00204a   
2019 Xu X, Ma Z, Duan R, Zou X. Predicting protein-ligand binding modes for CELPP and GC3: workflows and insight. Journal of Computer-Aided Molecular Design. PMID 30689079 DOI: 10.1007/s10822-019-00185-0   
2019 Porter JR, Moeder KE, Sibbald CA, Zimmerman MI, Hart KM, Greenberg MJ, Bowman GR. Cooperative Changes in Solvent Exposure Identify Cryptic Pockets, Switches, and Allosteric Coupling. Biophysical Journal. PMID 30744991 DOI: 10.1016/j.bpj.2018.11.3144   
2019 Pu L, Govindaraj RG, Lemoine JM, Wu HC, Brylinski M. DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network. Plos Computational Biology. 15: e1006718. PMID 30716081 DOI: 10.1371/journal.pcbi.1006718   
2019 Russell RW, Fritz MP, Kraus J, Quinn CM, Polenova T, Gronenborn AM. Accuracy and precision of protein structures determined by magic angle spinning NMR spectroscopy: for some 'with a little help from a friend'. Journal of Biomolecular Nmr. PMID 30847635 DOI: 10.1007/s10858-019-00233-9   
2019 Bhattacharya D. refineD: Improved protein structure refinement using machine learning based restrained relaxation. Bioinformatics (Oxford, England). PMID 30759180 DOI: 10.1093/bioinformatics/btz101   
2019 Islam ML, Shatabda S, Rashid MA, Khan MGM, Rahman MS. Protein structure prediction from inaccurate and sparse NMR data using an enhanced genetic algorithm. Computational Biology and Chemistry. 79: 6-15. PMID 30703679 DOI: 10.1016/j.compbiolchem.2019.01.004   
2019 Evangelista W, Ellingson SR, Smith JC, Baudry JY. Ensemble Docking in Drug Discovery: How Many Protein Configurations from Molecular Dynamics Simulations Are Needed to Reproduce Known Ligand Binding? The Journal of Physical Chemistry. B. PMID 30695645 DOI: 10.1021/acs.jpcb.8b11491   
2019 Orellana L, Gustavsson J, Bergh C, Yoluk O, Lindahl E. eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces. Bioinformatics (Oxford, England). PMID 30838394 DOI: 10.1093/bioinformatics/btz104   
2019 Faustino AF, Barbosa GM, Silva M, Castanho MARB, Da Poian AT, Cabrita EJ, Santos NC, Almeida FCL, Martins IC. Fast NMR method to probe solvent accessibility and disordered regions in proteins. Scientific Reports. 9: 1647. PMID 30733478 DOI: 10.1038/s41598-018-37599-z   
2019 Fobe TL, Kazakov A, Riccardi D. Cys.sqlite: A Structured-Information Approach to the Comprehensive Analysis of Cysteine Disulfide Bonds in the Protein Databank. Journal of Chemical Information and Modeling. PMID 30694665 DOI: 10.1021/acs.jcim.8b00950   
2019 Ludwiczak J, Winski A, Szczepaniak K, Alva V, Dunin-Horkawicz S. DeepCoil - a fast and accurate prediction of coiled-coil domains in protein sequences. Bioinformatics (Oxford, England). PMID 30601942 DOI: 10.1093/bioinformatics/bty1062   
2019 Bauer MR, Mackey MD. Electrostatic Complementarity as a Fast and Effective Tool to Optimize Binding and Selectivity of Protein-Ligand Complexes. Journal of Medicinal Chemistry. PMID 30807144 DOI: 10.1021/acs.jmedchem.8b01925   
2019 Qi HW, Kulik HJ. Evaluating Unexpectedly Short Non-covalent Distances in X-ray Crystal Structures of Proteins with Electronic Structure Analysis. Journal of Chemical Information and Modeling. PMID 30875210 DOI: 10.1021/acs.jcim.9b00144   
2019 Tripler TN, Kaplan AR, Alexandrescu AT, Teschke CM. Conservation and divergence of the I-domain inserted into the ubiquitous HK97 coat protein fold in the P22-like bacteriophages. Journal of Virology. PMID 30787158 DOI: 10.1128/JVI.00007-19   
2019 Lombardo CM, Kumar M V V, Douat C, Rosu F, Mergny JL, Salgado GF, Guichard G. Design and Structure Determination of a Composite Zinc Finger Containing a Nonpeptide Foldamer Helical Domain. Journal of the American Chemical Society. 141: 2516-2525. PMID 30715863 DOI: 10.1021/jacs.8b12240   
2019 Isa DM, Chin SP, Chong WL, Zain SM, Rahman NA, Lee VS. Dynamics and binding interactions of peptide inhibitors of dengue virus entry. Journal of Biological Physics. PMID 30680580 DOI: 10.1007/s10867-018-9515-6   
2019 Leone V, Waclawska I, Kossmann K, Koshy C, Sharma M, Prisner TF, Ziegler C, Endeward B, Forrest LR. Interpretation of spectroscopic data using molecular simulations for the secondary active transporter BetP. The Journal of General Physiology. PMID 30728216 DOI: 10.1085/jgp.201812111   
2019 Nath V, Agrawal R, Kumar V. Structure based Docking and Molecular dynamics studies: Peroxisome proliferator-activated receptors -α/γ dual agonists for treatment of metabolic disorders. Journal of Biomolecular Structure & Dynamics. 1-14. PMID 30767625 DOI: 10.1080/07391102.2019.1581089   
2019 Markwick PRL, Peacock RB, Komives EA. Accurate Prediction of Amide Exchange in the Fast Limit Reveals Thrombin Allostery. Biophysical Journal. 116: 49-56. PMID 30558884 DOI: 10.1016/j.bpj.2018.11.023   
2019 Wang CK, Craik DJ. Towards Structure Determination of Disulfide-Rich Peptides Using Chemical Shift-Based Methods. The Journal of Physical Chemistry. B. PMID 30730741 DOI: 10.1021/acs.jpcb.8b10649   
2019 Freiberger MI, Guzovsky AB, Wolynes PG, Parra RG, Ferreiro DU. Local frustration around enzyme active sites. Proceedings of the National Academy of Sciences of the United States of America. PMID 30765513 DOI: 10.1073/pnas.1819859116   
2019 Wood D, Lopez-Fernandez JD, Knight L, Al-Khawaldeh I, Gai C, Lin S, Martin MP, Miller D, Cano C, Endicott J, Hardcastle I, Noble M, Waring MJ. FragLites - minimal, halogenated fragments displaying pharmacophore doublets. An efficient approach to druggability assessment and hit generation. Journal of Medicinal Chemistry. PMID 30860382 DOI: 10.1021/acs.jmedchem.9b00304   
2019 Codina N, Hilton D, Zhang C, Chakroun N, Ahmad SS, Perkins SJ, Dalby PA. An Expanded Conformation of an Antibody Fab Region by X-Ray Scattering, Molecular Dynamics and smFRET Identifies an Aggregation Mechanism. Journal of Molecular Biology. PMID 30776431 DOI: 10.1016/j.jmb.2019.02.009   
2019 Brown ZP, Takagi J. Advances in domain and subunit localization technology for electron microscopy. Biophysical Reviews. PMID 30834502 DOI: 10.1007/s12551-019-00513-6   
2019 Blinov N, Wishart DS, Kovalenko A. Solvent Composition Effects on Structural Properties of the A β42 Monomer From the 3D-RISM-KH Molecular Theory of Solvation. The Journal of Physical Chemistry. B. PMID 30811210 DOI: 10.1021/acs.jpcb.9b00480   
2019 Patterson A, Tokmina-Lukaszewska M, Bothner B. Probing Cascade complex composition and stability using native mass spectrometry techniques. Methods in Enzymology. 616: 87-116. PMID 30691656 DOI: 10.1016/bs.mie.2018.10.018   
2019 Oliver D, Michaelis M, Heinz H, Volkov VV, Perry CC. From phage display to structure: an interplay of enthalpy and entropy in the binding of the LDHSLHS polypeptide to silica. Physical Chemistry Chemical Physics : Pccp. PMID 30747204 DOI: 10.1039/c8cp07011c   
2019 Liu Z, Cui Y, Xiong Z, Nasiri A, Zhang A, Hu J. DeepSeqPan, a novel deep convolutional neural network model for pan-specific class I HLA-peptide binding affinity prediction. Scientific Reports. 9: 794. PMID 30692623 DOI: 10.1038/s41598-018-37214-1   
2019 Li J, Fu A, Zhang L. An Overview of Scoring Functions Used for Protein-Ligand Interactions in Molecular Docking. Interdisciplinary Sciences, Computational Life Sciences. PMID 30877639 DOI: 10.1007/s12539-019-00327-w   
2019 Sheng J, Olrichs NK, Geerts WJ, Li X, Rehman AU, Gadella BM, Kaloyanova DV, Helms B. Zinc binding regulates amyloid-like aggregation of GAPR-1. Bioscience Reports. PMID 30700571 DOI: 10.1042/BSR20182345   
2019 Bari KJ, Sharma S, Chary KVR. Conformational dynamics study on human γS-crystallin as an efficient route to childhood blindness. Biochemical and Biophysical Research Communications. PMID 30827504 DOI: 10.1016/j.bbrc.2019.02.124   
2019 Wang W, Wang D. Extreme Fuzziness: Direct Interactions between Two IDPs. Biomolecules. 9. PMID 30813629 DOI: 10.3390/biom9030081   
2019 Liu X, Fuentes EJ. Emerging Themes in PDZ Domain Signaling: Structure, Function, and Inhibition. International Review of Cell and Molecular Biology. 343: 129-218. PMID 30712672 DOI: 10.1016/bs.ircmb.2018.05.013   
2019 Modi V, Dunbrack RL. Defining a new nomenclature for the structures of active and inactive kinases. Proceedings of the National Academy of Sciences of the United States of America. PMID 30867294 DOI: 10.1073/pnas.1814279116   
2019 Li Z, Yan F, Miao Q, Meng Y, Wen L, Jiang Q, Zhou P. Self-binding Peptides: Binding-upon-Folding versus Folding-upon-Binding. Journal of Theoretical Biology. PMID 30802465 DOI: 10.1016/j.jtbi.2019.02.014   
2019 Larzábal M, Baldoni HA, Suvire FD, Curto LM, Gomez GE, Da Silva WM, Giudicessi SL, Camperi SA, Delfino JM, Cataldi AA, Enriz D. An inhibitory mechanism of action of coiled-coil peptides against type three secretion system from enteropathogenic Escherichia coli. Journal of Peptide Science : An Official Publication of the European Peptide Society. e3149. PMID 30746861 DOI: 10.1002/psc.3149   
2019 Machado MR, Barrera EE, Klein F, Sóñora M, Silva S, Pantano S. The SIRAH force field 2.0: Altius, Fortius, Citius. Journal of Chemical Theory and Computation. PMID 30810317 DOI: 10.1021/acs.jctc.9b00006   
2019 Lee HS, Im W. Stalis: A Computational Method for Template-Based Ab Initio Ligand Design. Journal of Computational Chemistry. PMID 30829435 DOI: 10.1002/jcc.25813